octavmethods {sads}  R Documentation 
Creates an object of octavclass
with number of
species in octaves of abundances from a vector
of abundances or from a fitted model.
octav(x, oct, preston=FALSE)
x 
a numerical vector of abundances or an object of class

oct 
integer vector; the octaves to tabulate abundances. Should
include all abundance values in 
preston 
logical; if 'TRUE' use Preston method to count
frequencies (see details), if 'FALSE' class intervals are open on
the left (default in 
Preston (1948) popularized the use of histograms with
logarithmic classes to depict species abundance distributions
(Magurran 1989). Preston used classes at log base two, which he called
‘octaves’ as their endpoints double from one class to the other. In
Preston original method half of the species with abundances equal to the
limits of octaves are credited to the neighboring octave. If
preston=TRUE
this nonstandard method of class closure is
applied. In general this makes the histogram more
bellshaped, as Preston expected (see example).
an object of class octav
, which is a data frame with three vectors:
octav 
integer; octave number, which is the upper limit of the class in log2. 
upper 
numeric; upper limit of the class in arithmetic scale. 
Freq 
integer or numeric; (relative) frequencies of species in each class. 
signature(x = "numeric")
number of species in each octave in a vector of species abundances.
signature(x = "fitsad")
number of species in each octave
in the original abundance vector used to fit a model with fitsad
.
signature(x = "fitrad")
number of species in each octave
in the original abundance vector used to fit a model with fitrad
.
Paulo I Prado prado@ib.usp.br, Andre Chalom and Murilo Dantas Miranda
Magurran, A.E. 1989. Ecological diversity and its measurement. Princeton University Press.
Preston, F.W. 1948. The commonness and rarity of species. Ecology 29: 254–283.
octavclass
for methods to create an octave
plot; octavpred
to get an octav
object of
predicted abundances from a theoretical distribution; fitsadclass
and
fitradclass
objects, from which you can also get an
object of class octav
; man page of prestonfit
in package vegan for a
detailed account of Preston's octaves and an alternative way to get
octaves and fitting of species abundances distributions.
## BCI tree data (bci.oc1 < octav(bci, preston=TRUE)) ## Comparing with standard class closure par(mfrow=c(1,2)) plot(octav(bci), main="octav(bci, preston=FALSE)") plot(bci.oc1, main="octav(bci, preston=TRUE)") par(mfrow=c(1,1))